If you want those things to all fall into "AsisCore", then you need to use "@package AsisCore" for everything rather than including the Subfolder pieces in the package name.
Whatever you use as the "package" name is what will be used to group classes together. By including those Subfolder pieces in the package name string, you are telling phpDocumentor to treat, for example, "AsisCore_Template" as something separate and unrelated to "AsisCore_Template_Helpers_Loop".
Looking over the list of your output, I'd probably choose to include either zero, or at most one, Subfolder level in the package name. When you then view one package's main page, you'll see that the class names themselves help group things together in the listing order, simply because you are following the PSR-0 / PEAR naming convention.